R/other.normalization.R

In NanoStringNorm: Normalize NanoString miRNA and mRNA Data

# The NanoStringNorm package is copyright (c) 2012 Ontario Institute for Cancer Research (OICR)
# This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL
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other.normalization <- function(x, anno, OtherNorm = 'none', verbose = TRUE, genes.to.fit = NA, genes.to.predict = NA, ...) { 

	if (OtherNorm == 'quantile') {
		x = other.normalization.quantile(x, anno, OtherNorm, verbose = verbose, genes.to.fit = genes.to.fit);
		}
	else if (OtherNorm == 'zscore') {
		x = other.normalization.zscore(x, anno, OtherNorm, verbose = verbose, genes.to.fit = genes.to.fit);
		}
	else if (OtherNorm == 'rank.normal') {
		x = other.normalization.rank.normal(x, anno, OtherNorm, verbose = verbose, genes.to.fit = genes.to.fit);
		}
	else if (OtherNorm == 'vsn') {
		x = other.normalization.vsn(x, anno, OtherNorm, verbose = verbose, genes.to.fit = genes.to.fit, genes.to.predict);
		}
	else if (OtherNorm == 'none') {
		return(x);
		}
	else {
		stop(paste('OtherNorm:  The OtherNorm option', OtherNorm, 'is not implemented try using one of quantile, zscore, rank.normal, vsn.'));
		}

	return(x);
	}